Conformational Changes of a Single Semiflexible Macromolecule Near an Adsorbing Surface: A Monte Carlo Simulation (original) (raw)
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Chain stiffness bridges conventional polymer and bio-molecular phases
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Chain molecules play important roles in industry and in living cells. Our focus here is on distinct ways of modeling the stiffness inherent in a chain molecule. We consider three types of stiffnesses – one yielding an energy penalty for local bends (energetic stiffness) and the other two forbidding certain classes of chain conformations (entropic stiffness). Using detailed Wang-Landau microcanonical Monte Carlo simulations, we study the interplay between the nature of the stiffness and the ground state conformation of a self-attracting chain. We find a wide range of ground state conformations including a coil, a globule, a toroid, rods, helices, zig-zag strands resembling β-sheets, as well as knotted conformations allowing us to bridge conventional polymer phases and biomolecular phases. An analytical mapping is derived between the persistence lengths stemming from energetic and entropic stiffness. Our study shows unambiguously that different stiffness play different physical roles ...
Effects of Stiffness on Short, Semiflexible Homopolymer Chains
International Journal of Modern Physics C, 2012
Conformational and transition behavior of finite, semiflexible homopolymers is studied using an extension of the Wang–Landau algorithm. Generation of a flat distribution in the sampling parameters energy and stiffness allows for efficient investigation of transitions between various conformational phases. Of particular importance is the ability to predict behavior for a given stiffness value, where three classes of minimum energy conformations are expected: Solid-globular, rod-like and toroidal. We present first results highlighting the behavior of a single N = 20 length chain.
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The Journal of Chemical Physics, 2008
A polymer chain tethered to a surface may be compact or extended, adsorbed or desorbed, depending on interactions with the surface and the surrounding solvent. This leads to a rich phase diagram with a variety of transitions. To investigate these transitions we have performed Monte Carlo simulations of a bond-fluctuation model with Wang-Landau and umbrella sampling algorithms in a two-dimensional state space. The simulations' density of states results have been evaluated for interaction parameters spanning the range from good to poor solvent conditions and from repulsive to strongly attractive surfaces. In this work, we describe the simulation method and present results for the overall phase behavior and for some of the transitions. For adsorption in good solvent, we compare with Metropolis Monte Carlo data for the same model and find good agreement between the results. For the collapse transition, which occurs when the solvent quality changes from good to poor, we consider two situations corresponding to three-dimensional (hard surface) and twodimensional (very attractive surface) chain conformations, respectively. For the hard surface, we compare tethered chains with free chains and find very similar behavior for both types of chains. For the very attractive surface, we find the two-dimensional chain collapse to be a two-step transition with the same sequence of transitions that is observed for three-dimensional chains: a coil-globule transition that changes the overall chain size is followed by a local rearrangement of chain segments.
Makromolekulare Chemie. Macromolecular Symposia, 1991
7'he relaxation PrOP6I'tieS Of polymer chains L n the nematic LC-state or In the external q u a k p o l e field may depend both on the variation of the conformation in the ordered state and on the activation barrier of the molecular (or external) field .This barrier should be surmounted during reorientation of chain elements. The lattice model theory of chain stiffening of macromolecules in the LC-state is proposed. The calculation and comparison of tho longitudinal and transversal relaxatlon spectra fur the continuous and discrete rotameric mechanism of the mobility are gerfonned. For the simplest model of hetorogeneous polymer chain the possibility of the more complex relaxational behavior i.e. the existence of two longitudinal and two transversal relaxation specbra w a s shown.
Influence of Surface Interactions on Folding and Forced Unbinding of Semiflexible Chains
The Journal of Physical Chemistry B, 2005
We have investigated the folding and forced unbinding transitions of adsorbed semiflexible polymer chains using theory and simulations. These processes describe, at an elementary level, a number of biologically relevant phenomena that include adhesive interactions between proteins and tethering of receptors to cell walls. The binding interface is modeled as a solid surface, and the wormlike chain (WLC) is used for the semiflexible chain (SC). Using Langevin simulations, in the overdamped limit we examine the ordering kinetics of racquet-like and toroidal structures in the presence of an attractive interaction between the surface and the polymer chain. For a range of interactions, temperature, and the persistence length, l p , we obtained the monomer density distribution, n(x), (x is the perpendicular distance of a tagged chain end from the surface) for all of the relevant morphologies. There is a single peak in n(x) inside the range of attractive forces, b, for chains in the extended conformations, whereas in racquet and toroidal structures there is an additional peak at x ≈ b. The simulated results for n(x) are in good agreement with theory.
Universal monomer dynamics of a two-dimensional semi-flexible chain
EPL (Europhysics Letters), 2014
We present a unified scaling theory for the dynamics of monomers for dilute solutions of semiflexible polymers under good solvent conditions in the free draining limit. Our theory encompasses the well-known regimes of mean square displacements (MSDs) of stiff chains growing like t 3/4 with time due to bending motions, and the Rouse-like regime t 2ν/(1+2ν) where ν is the Flory exponent describing the radius R of a swollen flexible coil. We identify how the prefactors of these laws scale with the persistence length ℓp, and show that a crossover from stiff to flexible behavior occurs at a MSD of order ℓ 2 p (at a time proportional to ℓ 3 p). A second crossover (to diffusive motion) occurs when the MSD is of order R 2. Large scale Molecular Dynamics simulations of a bead-spring model with a bond bending potential (allowing to vary ℓp from 1 to 200 Lennard-Jones units) provide compelling evidence for the theory, in D = 2 dimensions where ν = 3/4. Our results should be valuable for understanding the dynamics of DNA (and other semiflexible biopolymers) adsorbed on substrates.
Polymers
The combination of flexibility and semiflexibility in a single molecule is a powerful design principle both in nature and in materials science. We present results on the conformational behavior of a single multiblock-copolymer chain, consisting of equal amounts of Flexible (F) and Semiflexible (S) blocks with different affinity to an implicit solvent. We consider a manifold of macrostates defined by two terms in the total energy: intermonomer interaction energy and stiffness energy. To obtain diagrams of states (pseudo-phase diagrams), we performed flat-histogram Monte Carlo simulations using the Stochastic Approximation Monte Carlo algorithm (SAMC). We have accumulated two-Dimensional Density of States (2D DoS) functions (defined on the 2D manifold of macrostates) for a SF-multiblock-copolymer chain of length N = 64 with block lengths b = 4, 8, 16, and 32 in two different selective solvents. In an analysis of the canonical ensemble, we calculated the heat capacity and determined it...
Effective stiffness and formation of secondary structures in a protein-like model
The Journal of chemical physics, 2016
We use Wang-Landau and replica exchange techniques to study the effect of an increasing stiffness on the formation of secondary structures in protein-like systems. Two possible models are considered. In both models, a polymer chain is formed by tethered beads where non-consecutive backbone beads attract each other via a square-well potential representing the tendency of the chain to fold. In addition, smaller hard spheres are attached to each non-terminal backbone bead along the direction normal to the chain to mimic the steric hindrance of side chains in real proteins. The two models, however, differ in the way bending rigidity is enforced. In the first model, partial overlap between consecutive beads is allowed. This reduces the possible bending angle between consecutive bonds thus producing an effective entropic stiffness that competes with a short-range attraction, and leads to the formation of secondary structures characteristic of proteins. We discuss the low-temperature phase...
Collapsed and Adsorbed States of a Directed Polymer Chain in Two Dimensions
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A phase diagram for a surface interacting long flexible partially directed polymer chain in a two-dimensional poor solvent where the possibility of collapse in the bulk exists is determined using exact enumeration method. We used a model of self attracting self-avoiding walk and evaluated 30 steps in series. An intermediate phase in between the desorbed collapsed and adsorbed expanded phases having the conformation of a surface attached globule is found. The four phases, viz. (i) desorbed expanded, (ii) desorbed collapsed, (iii) adsorbed expanded, (iv) surface attached globule are found to meet at a multicritical point. These features are in agreement with those of an isotropic (or non directed) polymer chain.